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. Author manuscript; available in PMC: 2017 Jul 1.
Published in final edited form as: Methods. 2016 Apr 12;103:157–166. doi: 10.1016/j.ymeth.2016.04.003

Table 1.

Characteristics shRNA designs

Design Structure Promoter Depends on Drosha Depends on Dicer Advantages / Disadvantages
Pre-miRNA-like “1st generation” Pre-miRNA Pol III ✗ ✓ + Well-characterized system
−Competition with endogenous miRNA pathway
−Lack promoter-directed specificity
Pri-miRNA-like “2nd generation” Pri-miRNA Pol II / III ✓ ✓ + Potential promoter-driven cell-type specificity
−Complicated processing
− Mirtron-based + Mirtron Pol II ✗ ✓ + Expressed within host mRNA transcripts
− Alternative splicing / specific regulation?
− Cluster mimic + Cluster Pol II ✓ ✓ + Multiplexed expression of various shRNAs
− Interdependencies within individual shRNAs
Ago-shRNA miR-451 Pol II / III ✓ ✗ + Guide strand is loaded into AGO2
+ Restrict off-targets effects of passenger strand
−Variable 3′-5′ exonucleolytic activity (23–26 nt mature)